Neutral sucrose gradient sedimentation of very large DNA from Bacillus subtilis. II. Double-strand breaks formed by gamma ray irradiation of the cells

The miRNA Content of Bone Marrow-Derived Extracellular Vesicles Contributes to Protein Pathway Alterations Involved in Ionising Radiation-Induced Bystander Responses

Extracellular vesicles (EVs), through their cargo, are important mediators of bystander responses in the irradiated bone marrow (BM). MiRNAs carried by EVs can potentially alter cellular pathways in EV-recipient cells by regulating their protein content. Using the CBA/Ca mouse model, we characterised the miRNA content of BM-derived EVs from mice irradiated with 0.1 Gy or 3 Gy using an nCounter analysis system. We also analysed proteomic changes in BM cells either directly irradiated or treated with EVs derived from the BM of irradiated mice. Our aim was to identify key cellular processes in the EV-acceptor cells regulated by miRNAs. The irradiation of BM cells with 0.1 Gy led to protein alterations involved in oxidative stress and immune and inflammatory processes. Oxidative stress-related pathways were also present in BM cells treated with EVs isolated from 0.1 Gy-irradiated mice, indicating the propagation of oxidative stress in a bystander manner. The irradiation of BM cells with 3 Gy led to protein pathway alterations involved in the DNA damage response, metabolism, cell death and immune and inflammatory processes. The majority of these pathways were also altered in BM cells treated with EVs from mice irradiated with 3 Gy. Certain pathways (cell cycle, acute and chronic myeloid leukaemia) regulated by miRNAs differentially expressed in EVs isolated from mice irradiated with 3 Gy overlapped with protein pathway alterations in BM cells treated with 3 Gy EVs. Six miRNAs were involved in these common pathways interacting with 11 proteins, suggesting the involvement of miRNAs in the EV-mediated bystander processes. In conclusion, we characterised proteomic changes in directly irradiated and EV-treated BM cells, identified processes transmitted in a bystander manner and suggested miRNA and protein candidates potentially involved in the regulation of these bystander processes.

Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways

Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.

Ionizing-radiation induced DNA double-strand breaks: a direct and indirect lighting up

The occurrence of DNA double-strand breaks (DSBs) induced by ionizing radiation has been extensively studied by biochemical or cell imaging techniques. Cell imaging development relies on technical advances as well as our knowledge of the cell DNA damage response (DDR) process. The DDR involves a complex network of proteins that initiate and coordinate DNA damage signaling and repair activities. As some DDR proteins assemble at DSBs in an established spatio-temporal pattern, visible nuclear foci are produced. In addition, post-translational modifications are important for the signaling and the recruitment of specific partners at damaged chromatin foci. We briefly review here the most widely used methods to study DSBs. We also discuss the development of indirect methods, using reporter expression or intra-nuclear antibodies, to follow the production of DSBs in real time and in living cells.

Visual quantification of DNA double-strand breaks in bacteria

In this paper, we describe a method for the visualization of double-strand breaks in a single electrostretched Escherichia coli DNA molecule. We also provide evidence that electrostretched or migrated DNA under neutral microgel electrophoresis conditions is made up of individual chromosomes. Using the neutral microgel electrophoresis technique, DNA migration (stretching) was measured and the number of DNA double-strand breaks were counted following exposure of E. coli cells to 0, 12.5, 25, 50, or 100 rad of X-rays. The use of an intense fluorescent dye, YOYO and custom-made slides have helped us in visualizing individual bacterial DNA molecules. Bacterial DNA appears similar in structure compared to electrostretched DNA from human lymphocytes. We were able to detect changes in DNA migration (stretching) induced by an X-ray dose as low as 12.5 rad and an increase in the number of DNA breaks induced by a dose as low as 25 rad. The extent of DNA migration and number of breaks were directly correlated to X-ray dosage.

Localization of a DNA repair gene (XRCC5) involved in double-strand-break rejoining to human chromosome 2

Complementation of the repair defect in hamster xrs mutants has been achieved by transfer of human chromosome 2 using the method of microcell-mediated chromosome transfer. The xrs mutants belong to ionizing radiation complementation group 5, are highly sensitive to ionizing radiation, and have an impaired ability to rejoin radiation-induced DNA double-strand breaks. Both phenotypes were corrected by chromosome 2, although the correction of radiation sensitivity was only partial. Complementation was achieved in two members of this complementation group, xrs6 and XR-V15B, derived independently from the CHO and V79 cell lines, respectively. The presence of human chromosome 2 in complemented clones was examined cytogenetically and by PCR analysis with primers directed at a human-specific long interspersed repetitive sequence or chromosome 2-specific genes. Complementation was observed in 25/27 hybrids, one of which contained only the q arm of chromosome 2. The two noncomplementing hybrids were missing segments of chromosome 2. The use of a back-selection system enabled the isolation of clones that had lost the human chromosome and these regained radiation sensitivity. Transfer of several other human chromosomes did not result in complementation of the repair defect in XR-V15B. These data show that the gene defective in xrs cells, XRCC5, which is involved in double-strand break rejoining, is located on human chromosome 2q.

Heavy ion induced double strand breaks in bacteria and bacteriophages

DNA damage induced by heavy ions in bacterial cells and bacteriophages such as Bacillus subtilis, E. coli and Bacteriophage T1 were investigated by analyzing the double strand breaks in the chromosomal DNA. This kind of lesion is considered as one of the main reasons for lethal events. To analyze double strand breaks in long molecules of DNA--up to some Mbp in length--the technique of pulse field agarose gel electrophoresis has been used. This allows the detection of one double strand break per genome. Cell lysis and DNA isolation were performed in small agarose blocks directly. This procedure secured minimum DNA destruction by shearing forces. After running a gel, the DNA was stained with ethidium bromide. The light intensity of ethidium bromide fluorescence for both the outcoming (running) DNA and the remaining intact DNA were measured by scanning. The mean number of double strand breaks was calculated by determining the quotient of these intensities. Strand break induction after heavy ion and X-ray irradiation was compared.

Studies on mammalian mutants defective in rejoining double-strand breaks in DNA

Mutants with defects in the rejoining of DNA double-strand breaks (dsbs) have been identified and characterised from E. coli and the yeast, Saccharomyces cerevisiae. More recently, 3 mammalian cell mutants with defective dsb rejoining have also been described. These mutants are xrs, XR-1 and L5178Y/S, and they are derived from at least two distinct complementation groups. The aim of this article is to review the current status of the studies with these mammalian cell mutants which are defective in dsb rejoining and, in particular, to compare their properties with those mutants identified from lower organisms. Possible mechanistic differences in the process of dsb rejoining between prokaryotes and lower and higher eukaryotes are discussed. All the mammalian mutants defective in dsb rejoining, are sensitive primarily to ionising radiation with little cross-sensitivity to UV-radiation. This is similar to the rad52 mutants of S. cerevisiae but contrasts to the majority of the E. coli mutants with defective dsb rejoining. Where studied, the mammalian cell mutants show enhanced resistance to ionizing radiation in late S/G2 phase, which, in one case, correlates with an enhanced ability to rejoin dsbs. This, together with other evidence, suggests that two mechanisms of dsb rejoining may exist in higher eukaryotes, one which operates uniquely in S/G2 phase and a second mechanism operating throughout the cell cycle and dependent upon the xrs and XR-1 gene products (although whether the xrs and XR-1 dependent pathways are distinct cannot at present be ascertained). Since duplicate homologues will be present in late S/G2 phase cells, this pathway may involve a recombinational mechanism. The xrs-dependent pathway might involve illegitimate recombination, but the xrs mutants do not appear to have a major defect in homologous recombination (involving plasmid DNA) and in this respect are distinct from rad52 mutants.

Effect of mercaptoethylamine on DNA degradation in thermophilic bacteria bac. Stearothermophilus exposed to gamma-, UV-radiation or methylnitrosourea

The effect of mercaptoethylamine (MEA) on degradation of DNA in thermophilic bacteria Bac. stear. exposed to gamma-, UV-rays or methylnitrosourea (MNU) was studied. Using centrifugation on alkaline and neutral sucrose gradients, it was shown that MEA inhibits the accumulation of breaks in the DNA of Bac. stear. It also lowers the level of DNA degradation in toluene-treated cells of Bac. stear. under the action of the intrinsic nuclease, reduces the activity of the endonuclease specific for apurinic DNA, as well as that of S1-nuclease and DNase-I in vitro. The inhibition in the accumulation of DNA breaks is assumed to be due to a decrease of the endonuclease activity in the cells of thermophilic bacteria.

DNA double strand breaks in Ehrlich ascites tumour cells at low doses of x-rays. I. Determination of induced breaks by centrifugation at reduced speed

DNA double strand breaks (dsb) were determined in Ehrlich ascites tumour cells at doses down to 5 Gy. The method is based on the separation of DNA from other components by heating in a solution of pronase and detergents held in wide-mouth syringes, which were also used to facilitate the application of the released high molecular weight DNA to sucrose gradients. Purified DNA was sedimented in neutral sucrose gradients at low speed to reduce speed artifacts. The sedimentation profiles were analysed using a computer program and the number of dsb was determined by simulation of random breaks in the mass distribution of the control sample and by comparison of this simulated profile with that of the irradiated one. The number of dsb formed was proportional to X-ray dose in the range of 5 to 2000 Gy. The induction per dose was found to be nmr-1 D-1 = (11.7 +/- 2) x 10(-12) Gy-1.

Measurement of the kinetics of DNA double strand break repair in Ehrlich ascites tumour cells using the unwinding method

Two main components of DNA strand break repair have been found using the unwinding method. The first has a time constant (t37) of some minutes and the second, much slower component, a time constant of several hours. The time constant for the slower component of repair was found to vary with the conditions of incubation and to depend on the quality of the radiation. The t37 values obtained for slow repair under various conditions after X-irradiation and after alpha-irradiation were found to be close to those for repair of double strand breaks as measured by velocity sedimentation. Values for initial breaks, obtained by extrapolation of slow repair data back to time zero, were also close to those obtained for double strand breaks. We therefore propose that the unwinding method can be a useful technique for monitoring the repair of double strand breaks.

Repair of double-strand breaks and lethal damage in DNA of Ustilago maydis

The size of nuclear DNA from wild-typeUstilago maydiswas determined to be approximately 6·09 ± 0·3 × 108daltons from neutral sucrose gradient sedimentation analysis. Following exposure to ionizing radiation the nuclear DNA size was reduced due to the production of double-strand breaks in the DNA. These breaks were repaired when the irradiated cells were incubated in medium for at least one hour after irradiation. The repair was seen as a shift in the DNA profile from a low molecular weight region where the control DNA sedimented. Inhibition of protein synthesis by cycloheximide prevented this type of repair. Blocking protein synthesis also decreased the survival of irradiated wild-type cells but not radiation-sensitive mutants. Protein synthesis was necessary within the first one and a half hours after irradiation for the survival of wild-type cells to be unaffected. The results provide additional evidence for an inducible repair process inU. maydis.

Construction of a colony bank of E. coli containing hybrid plasmids representative of the Bacillus subtilis 168 genome. Expression of functions harbored by the recombinant plasmids in B. subtilis

A collection of about 2500 clones containing hybrid plasmids representative of nearly the entire genome of B. subtilis 168 was established in E. coli SK1592 by using the poly(dA).poly(dT) joining method with randomly sheared DNA fragments and plasmid pHV33, a bifunctional vector which can replicate in both E. coli and B. subtilis. Detection of cloned recombinant DNA molecules was based on the insertional inactivation of the Tc gene occurring at the unique BamHI cleavage site present in the vector plasmid. Thirty individual clones of the collection were shown to hybridize specifically with a B. subtilis rRNA probe. CCC-recombinant plasmids extracted from E. coli were pooled in lots of 100 and used to transform auxotrophic mutants of B. subtilis 168. Complementation of these auxotrophic mutations was observed for several markers such at thr, leuA, hisA, glyB and purB. In several cases, markers carried by the recombinant plasmids were lost from the plasmid and integrated into the chromosomal DNA. Loss of genetic markers from the hybrid plasmids did not occur when a rec- recipient strain of B. subtilis was used.

Interactions stabilizing DNA tertiary structure in the Escherichia coli chromosome investigated with ionizing radiation

The structure of the bacterial chromosome was investigated after introducing breaks in the DNA with gamma irradiation. It is demonstrated that irradiation of the chromosome in the cell prior to isolation results in partial unfolding of the isolated condensed DNA, while irradiation of the chromosome after it is released from the cell has no demonstrable effect on DNA folding. The results indicate that RNA/DNA interactions which stabilize DNA folds are unstable when breaks are introduced in the DNA prior to isolation of the chromosome. It is suggested that the supercoiled state of the DNA is required for the initial stabilization of some of the critical RNA/DNA interaction in the isolated nucleoid. However, some of these interactions are not affected by irradiation of the cells. Remnant supercoiling in partially relaxed chromosomes containing a limited number of DNA breaks has the same superhelical density as the unirradiated chromosome. This suggests that restraints on rotation of the packaged DNA are formed prior to the physical unwinding which occurs at the sites of the radiation induced DNA breads. - Analysis of the in vitro irradiated chromosomes shows that there are 100 +/- 30 domains of supercoiling per genome equivalent of DNA. The introduction of up to 50 double-strand breaks per nucleoid does not influence rotor speed effects of the sedimentation coefficient of the chromosome.

The production and repair of double strand breaks in cells from normal humans and from patients with ataxia telangiectasia

The production and repair of double strand breaks induced by gamma-rays in the DNA of human fibroblasts have been measured by sedimentation in sucrose radients under non-denaturing conditions. Unirradiated DNA formed a rapidly sedimenting gel. Low doses of radiation released freely sedimenting DNA molecules from this gel. Higher doses reduced the rate of sedimentation of the free DNA due to the introduction of double strand breaks. The breakage efficiency was 1 break/1.3 X 10(10) daltons of DNA/krad. Postirradiation incubation after a high dose of radiation resulted in an increase in molecular weight of the free DNA molecules, and after a low dose the rapidly-sedimenting gel was reformed. The data suggest that double strand breaks are repaired in human fibroblasts. No significant differences were found between fibroblasts from two normal donors and four patients with the radiosensitive disorder, ataxia telangiectasia, in either the production or repair of double strand breaks.

Dependence of the sedimentation of high molecular weight DNA on centrifuge speed

A theory by Zimm [B.H.Zimm, Biophys. Chem. 1-(1974)279] predicts that for a given centrifuge speed, there is a broad maximum in a plot of the sedimentation coefficient of DNA against molecular wight. Experimental measurements of these maxima for various centrifuge speeds were made for double-helical DNA in neutral sucrose gradients and singlestrand DNA in alkaline gradients. The measurements are in quantitative agreement with the theory, providing good evidence for its validity. The existence of the maximum shows that there is a limit to the sedimentation rate under specified conditions for KNA in the linear form. By implication, DNA observed to sediment faster than this limit is not in the linear form to which most sedimentation theory is applicable.

The repair of double-strand breaks in the nuclear DNA of Saccharomyces cerevisiae and its genetic control

With the use of neutral sucrose sedimentation techniques, the size of unirradiated nuclear DNA and the repair of double-strand breaks induced in it by ionizing radiation have been determined in both wild-type and homozygous rad52 diploids of the yeast Saccharomyces cerevisiae. The number average molecular weight of unirradiated DNA in these experiments is 3.0 X 10(8)+/-0.3 Daltons. Double-strand breaks are induced with a frequency of 0.58 X 10(-10) per Daltonkrad in the range of 25 to 100 krad. Since repair at low doses is observed in wild-type but not homozygous rad52 strains, the corresponding rad52 gene product is concluded to have a role in the repair process. Cycloheximide was also observed to inhibit repair to a limited extent indicating a requirement for protein synthesis. Based on the sensitivity of various mutants and the induction frequency of double-strand breaks, it is concluded that there are 1 to 2 double-strand breaks per lethal event in diploid cells incapable of repairing these breaks.

DNA breakage, repair and lethality after 125I decay in rec+ and recA strains of Escherichia coli

Iodine-125 decays by electron capture and is known to cause extensive molecular fragmentation via the Augur effect. 125I was incorporated into the DNA of exponentially-growing E. coli K12 AB2487, a recA mutant, and E. coli K12 AB2497, the corresponding rec+ strain, as 5-iododeoxyuridine (IUdR), an analogue of thymidine. Radioactive bacteria were stored at - 196 degrees C, and samples were periodically assayed for loss of viability and for the induction of double-strand breaks (DSBs) in DNA. Each 125I decay in the DNA of either strain induces one DSB, i.e. alpha(DSB) = 1.0. For the recA strain, alpha(lethal) = 0.9 and for the rec+ strain, 0.4. Assays for biological repair of DSBs, involving incubation of thawed samples in growth-medium at 37 degrees C before the extraction of DNA, demonstrate significant repair of 125I-induced DSBs by rec+ cells but none by recA cells. For small numbers of decays, there is approximately a 1:1 correlation, for either strain, between lethal decays and post-incubation residual DSBs. Comparison with data for larger numbers of decays indicates that a typical rec+ cell can repair no more than three to four DSBs per completed genome (2.5 x 10(9) daltons).

Enzymatic induction of DNA double-strand breaks in gamma-irradiated Escherichia coli K-12

The polA1 mutation increases the sensitivity of E. coli K-12 by killing by gamma-irradiation in air by a factor of 2.9 and increases the yield of DNA double-strand breaks by a factor of 2.5. These additional DNA double-strand breaks appear to be due to the action of nucleases in the polA1 strain rather than to the rejoining of radiation-induced double-strand breaks in the pol+ strain. This conclusion is based upon the observation that gamma-irradiation at 3 degrees did not affect the yield of DNA double-strand breaks in the pol+ strain, but decreased the yield in the polA1 strain by a factor of 2.2. Irradiation of the polA1 strain at 3 degrees followed by incubation at 3 degrees for 20 min before plating resulted in approximately a 1.5-fold increase in the D0. The yield of DNA double-strand breaks was reduced by a factor of 1.5. The pol+ strain, however, did not show the protective effect of the low temperature incubation upon either survival or DNA double-strand breakage. We suggest that the increased yield of DNA double-strand breaks in the polA1 strain may be the result of the unsuccessful exision repair of ionizing radiation-induced DNA base damage.

CHO cell repair of single-strand and double-strand DNA breaks induced by gamma- and alpha-radiations

Neutral and alkaline sucrose gradient sedimentation analysis was used to measure double- and single-strand breaks in the DNA of Chinese hamster ovary (CHO) cells exposed to either gamma- or alpha-radiation. After irradiation, cells were incubated for 15-180 min to test the ability of the cell to rejoin the DNA breaks. Essentially complete rejoining was observed for single-strand breaks induced by gamma- or alpha-doses below 20 krad and for double-strand breaks induced by gamma doses below 60 krad. Approximately 80% rejoining was observed for double-strand breaks induced by alpha doses below 40 krad. At higher doses, the repair system appeared to saturate in such a way that essentially no additional breaks were rejoined.

The repair of double-strand breaks in chromosomal DNA of yeast

Ionizing radiation induces double-strand breaks in the nuclear DNA of the yeast Saccharomyces cerevisiae with an efficiency of approximately 0.6 X 10(-10) breaks being repaired. Based on the efficiency of break production, the sensitivity of a rad52 mutant, and the absence of radiation-induced recombination in such a mutant, it is proposed that the corresponding gene product may be involved in double-strand break repair. A model involving recombination and DNA synthesis is described for this type of repair.